load_prv: Loads providers information into R.

In parseRPDR: Parse and Manipulate Research Patient Data Registry ('RPDR') Text Queries

Loads providers information into R.

Description

Loads providers information into the R environment.

Usage

load_prv(
  file,
  merge_id = "EMPI",
  sep = ":",
  id_length = "standard",
  perc = 0.6,
  na = TRUE,
  identical = TRUE,
  nThread = parallel::detectCores() - 1,
  mrn_type = TRUE
)

Arguments

file	string, full file path to Prv.txt.
merge_id	string, column name to use to create ID_MERGE column used to merge different datasets. Defaults to EPIC_PMRN, as it is the preferred MRN in the RPDR system.
sep	string, divider between hospital ID and MRN. Defaults to :.
id_length	string, indicating whether to modify MRN length based-on required values id_length = standard, or to keep lengths as is id_length = asis. If id_length = standard then in case of MGH, BWH, MCL, EMPI and PMRN the length of the MRNs are corrected accordingly by adding zeros, or removing numeral from the beginning. In other cases the lengths are unchanged. Defaults to standard.
perc	numeric, a number between 0-1 indicating which parsed ID columns to keep. Data present in perc x 100% of patients are kept.
na	boolean, whether to remove columns with only NA values. Defaults to TRUE.
identical	boolean, whether to remove columns with identical values. Defaults to TRUE.
nThread	integer, number of threads to use to load data.
mrn_type	boolean, should data in MRN_Type and MRN be parsed. Defaults to TURE only for Con.txt, as it is not advised to parse these for all data sources as it takes considerable time.

Value

data table, with provider information data.

ID_MERGE

numeric, defined IDs by merge_id, used for merging later.

ID_con_EMPI

string, Unique Partners-wide identifier assigned to the patient used to consolidate patient information from con datasource, corresponds to EMPI in RPDR. Data is formatted using pretty_mrn().

ID_con_PMRN

string, Epic medical record number. This value is unique across Epic instances within the Partners network from condatasource, corresponds to EPIC_PMRN in RPDR. Data is formatted using pretty_mrn().

ID_con_loc

string, if mrn_type == TRUE, then the data in MRN_Type and MRN are parsed into IDs corresponding to locations (loc). Data is formatted using pretty_mrn().

time_prv_last_seen

POSIXct, Date when the patient was last seen by the provider, corresponds to Last_Seen_Date in RPDR.

prv_name

string, Full name of the provider, corresponds to Provider_Name in RPDR.

prv_rank

string, Provides a quantitative value of provider's level of interaction with the patient. This is calculated using the number of CPT codes for face-to-face visits that the provider has billed for in relation to the patient, corresponds to Provider_Rank in RPDR.

prv_ID

string, Identification code for the provider, including the source institution, corresponds to Provider_ID in RPDR.

prv_ID_CMP

string, Corporate Provider Master ID. This is the unique identifier for a provider across the MGB network, corresponds to CPM_Id in RPDR.

prv_spec

string, Comma-delimited list of the provider's specialties, corresponds to Specialties in RPDR.

prv_pcp

string, Available for BWH and MGH PCPs only. Flag indicating whether the provider is listed as the patient's Primary Care Physician, corresponds to Is_PCP in RPDR.

prv_dep

string, Provider's department, corresponds to Enterprise_service in RPDR.

prv_address1

string, Address of the provider's primary practice, corresponds to Address_1 in RPDR.

prv_address2

string, Additional address information, corresponds to Address_2 in RPDR.

prv_city

string, City of the provider's primary practice, corresponds to City in RPDR.

prv_state

string, State of the provider's primary practice, corresponds to State in RPDR.

prv_zip

string, Mailing zip code of provider's primary practice, corresponds to Zip in RPDR.

prv_phone

string, Telephone number of the provider's primary practice, corresponds to Phone_Ext in RPDR.

prv_fax

string, Fax number of the provider's primary practice, corresponds to Fax in RPDR.

prv_email

string, Primary e-mail address for the provider, corresponds to Email in RPDR.

Examples

## Not run: 
#Using defaults
d_prv <- load_prv(file = "test_Prv.txt")

#Use sequential processing
d_prv <- load_prv(file = "test_Prv.txt", nThread = 1)

#Use parallel processing and parse data in
#MRN_Type and MRN columns (default in load_con) and keep all IDs
d_prv <- load_prv(file = "test_Prv.txt", nThread = 20, mrn_type = TRUE, perc = 1)

## End(Not run)

parseRPDR documentation built on March 31, 2023, 11:36 p.m.